3KRL Transferase Transferase Inhibitor date Nov 18, 2009
title Cfms Tyrosine Kinase In Complex With 5-Cyano-Furan-2-Carboxy [4-(4-Methyl-Piperazin-1-Yl)-2-Piperidin-1-Yl-Phenyl]-Amide
authors C.Schubert
compound source
Molecule: Macrophage Colony-Stimulating Factor 1 Receptor, Fibroblast Growth Factor Receptor 1;
Chain: A
Fragment: Unp Residues 538-678, 753-922
Synonym: C-Fms, Fgfr-1
Engineered: Yes
Mutation: Yes
Other_details: Native Kinase Insert Domain Of C-Fms Replace Receptor Kinase Insert Domain
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Csf1r, Fgfr1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: H 3
R_factor 0.209 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
81.111 81.111 142.570 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand KRL, SO4 enzyme Transferase E.C. BRENDA

Primary referenceOptimization of a Potent Class of Arylamide Colony-Stimulating Factor-1 Receptor Inhibitors Leading to Anti-inflammatory Clinical Candidate 4-Cyano-N-[2-(1-cyclohexen-1-yl)-4-[1-[(dimethylamino)acetyl]-4-piperidiny l]phenyl]-1H-imidazole-2-carboxamide (JNJ-28312141)., Illig CR, Manthey CL, Wall MJ, Meegalla SK, Chen J, Wilson KJ, Ballentine SK, Desjarlais RL, Schubert C, Crysler CS, Chen Y, Molloy CJ, Chaikin MA, Donatelli RR, Yurkow E, Zhou Z, Player MR, Tomczuk BE, J Med Chem. 2011 Nov 24;54(22):7860-83. Epub 2011 Oct 31. PMID:22039836
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (3krl.pdb1.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 3KRL
  • CSU: Contacts of Structural Units for 3KRL
  • Structure Factors (225 Kb)
  • Retrieve 3KRL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KRL from S2C, [Save to disk]
  • Re-refined 3krl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KRL in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3KRL
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3KRL, from MSDmotif at EBI
  • Fold representative 3krl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3krl] [3krl_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3KRL: [TyrKc ] by SMART
  • Other resources with information on 3KRL
  • Community annotation for 3KRL at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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